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Old 04-11-2019, 03:01 AM   #101
Chief_Lazy_Bison
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So I resubmitted the job on a node with 40 processors and 1TB of memory and I received two very similar exceptions and the job is hanging again.

Exception in thread "Thread-147" java.lang.AssertionError
at clump.KmerSort3$FetchThread3.fetchNext_inner(KmerSort3.java:706)
at clump.KmerSort3$FetchThread3.fetchNext(KmerSort3.java:655)
at clump.KmerSort3$FetchThread3.run(KmerSort3.java:577)
--
Exception in thread "Thread-146" java.lang.AssertionError
at clump.KmerSort3$FetchThread3.fetchNext_inner(KmerSort3.java:706)
at clump.KmerSort3$FetchThread3.fetchNext(KmerSort3.java:655)
at clump.KmerSort3$FetchThread3.run(KmerSort3.java:577)
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Old 04-11-2019, 03:53 AM   #102
GenoMax
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Can you provide the exact command line you are using? Is this being submitted via a job scheduler?
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Old 04-11-2019, 04:24 AM   #103
Chief_Lazy_Bison
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It is submitted to a SLURM queue via the attached script.

These reads are a collection of concatenated interleaved paired end libraries

The same script worked well on the individual libraries, but I wanted to do an assembly with all of the reads together so I concatenated them all with
Code:
cat *fq.gz > ALL.fq.gz
The command that ends up stalling is this:
Code:
clumpify.sh in=ALL_temp.fq.gz out=ALL.eccc.fq.gz ecc passes=4 reorder

bbmerge plows through these reads with no complaints just prior to clumpify

Code:
bbmerge.sh in=ALL_temp.fq.gz out=ALL.ecco.fq.gz ecco mix vstrict ordered ihist=ALL_ihist_merge1.txt
Attached Files
File Type: txt ALL_ec.SLURM.txt (6.5 KB, 1 views)
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Old 04-11-2019, 06:12 AM   #104
GenoMax
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I think you should follow the order of tools that Brian has in his script example. Do clumpify job first. Since you are merging the reads first I am going to speculate that clumpify is unable to identify duplicates properly. If your data in not from a patterned flowcell you could remove the "optical" flag for clumpify.
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Old 04-15-2019, 03:17 AM   #105
Chief_Lazy_Bison
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Thank you for the quick advice. I had attempted to merge many samples together at the front end of the pipeline so that I could to all the QC and error correction at once. My problem was fixed when I did QC and error correction on each sample individually and then merged for a co-assembly.

Thanks again.
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